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- PDB-7wsz: human glyoxalase I (with C-ter His tag) in glycerol-bound form -

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Basic information

Entry
Database: PDB / ID: 7wsz
Titlehuman glyoxalase I (with C-ter His tag) in glycerol-bound form
ComponentsLactoylglutathione lyase
KeywordsLYASE / glyoxalase I / zinc metalloenzyme
Function / homology
Function and homology information


lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding ...lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Glyoxalase I signature 2. / Glyoxalase I / Glyoxalase I, conserved site / Glyoxalase I signature 1. / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / BORIC ACID / IMIDAZOLE / Lactoylglutathione lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsUsami, M. / Ando, K. / Yokoyama, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K07316 Japan
CitationJournal: Febs Lett. / Year: 2022
Title: Crystal structures of human glyoxalase I and its complex with TLSC702 reveal inhibitor binding mode and substrate preference.
Authors: Usami, M. / Ando, K. / Shibuya, A. / Takasawa, R. / Yokoyama, H.
History
DepositionFeb 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactoylglutathione lyase
B: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,66014
Polymers43,7502
Non-polymers91012
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-132 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.225, 96.995, 46.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 8 - 180 / Label seq-ID: 9 - 181

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lactoylglutathione lyase / Aldoketomutase / Glyoxalase I / Glx I / Ketone-aldehyde mutase / Methylglyoxalase / S-D- ...Aldoketomutase / Glyoxalase I / Glx I / Ketone-aldehyde mutase / Methylglyoxalase / S-D-lactoylglutathione methylglyoxal lyase


Mass: 21874.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04760, lactoylglutathione lyase

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Non-polymers , 6 types, 299 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BH3O3
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MIB (sodium malonate, imidazole, and boric acid), 25% PEG1500

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.52→20 Å / Num. obs: 56869 / % possible obs: 95.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 18.7
Reflection shellResolution: 1.52→1.6 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.2 / % possible all: 71.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VW9

3vw9


Resolution: 1.52→19.9 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.437 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.187 5737 10.1 %RANDOM
Rwork0.161 ---
obs0.164 51062 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.52→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 51 287 3187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132958
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172718
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.6483975
X-RAY DIFFRACTIONr_angle_other_deg1.5461.5926349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4425355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70224.041146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6815526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9251510
X-RAY DIFFRACTIONr_chiral_restr0.10.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5244 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 243 -
Rwork0.312 2214 -
obs--56.88 %

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